Nucleotide diversity of a ND5 fragment confirms that population expansion is the most suitable explanation for the mtDNA haplotype polymorphism of Drosophila subobscura

AbstractOver the last 40 years, many types of population genetic markers have been used to assess the population structure of the pest moth species Helicoverpa armigera. While this species is highly vagile, there is evidence of inter-continental population structure. Here, we examine Z-chromosome molecular markers within and between Chinese and Australian populations. Using 1352 polymorphic sites from 40 Z-linked loci, we compared two Chinese populations of moths separated by 700 km and found virtually no population structure (n = 41 and n = 54, with <1% of variation discriminating between populations). The levels of nucleotide diversity within these populations were consistent with previous estimates from introns in Z-linked genes of Australian samples (π = 0.028 vs. 0.03). Furthermore, all loci surveyed in these Chinese populations showed a skew toward rare variants, with ten loci having a significant Tajima's D statistic, suggesting that this species could have undergone a population expansion. Eight of the 40 loci had been examined in a previous study of Australian moths, of which six revealed very little inter-continental population structure. However, the two markers associated with the Cyp303a1 locus that has previously been proposed to be a target of a selective sweep, exhibited allele structuring between countries. Using a separate dataset of 19 Australian and four Chinese moths, we scanned the molecular variation distributed across the entire Z-chromosome and found distinct blocks of differentiation that include the region containing Cyp303a1. We recommend some of these loci join those associated with insecticide resistance to form a set of genes best suited to analyzing population structure in this global pest.

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Maternal variability of Croatian Spotted goat (Capra hircus)

Czech Journal of Animal Science ◽

10.17221/240/2018-cjas ◽

2019 ◽

Vol 64 (No. 6) ◽

pp. 248-254

Author(s):

Ivana Drzaic ◽

Ino Curik ◽

Dinko Novosel ◽

Vlatka Cubric-Curik

Keyword(s):

Mitochondrial Dna ◽

Nucleotide Diversity ◽

Population Expansion ◽

Capra Hircus ◽

Phylogeographic Structure ◽

Goat Breed ◽

Loop Region ◽

D Loop ◽

Mtdna Diversity

Abstract: This study provides the first characterization of maternal ancestry and mitochondrial DNA (mtDNA) diversity in the Croatian Spotted goat (CSG), the most important autochthonous goat breed in Croatia. CSG (n = 25) were randomly sampled from seven herds and a 660-bp fragment from the mtDNA D-loop region was sequenced. Those sequences were compared with 122 corresponding GenBank sequences from goat populations in Albania, Austria, Egypt, Greece, Italy, Romania and Switzerland. CSG showed a great polymorphism (only three out of 17 haplotypes were shared) with high a haplotype (Hd = 0.967 ± 0.019) and nucleotide diversity (π = 0.01305 ± 0.00068). When compared with Mediterranean and ancient goats, all of the 25 CSG were randomly scattered inside haplogroup A showing the weak phylogeographic structure with within-breed variance accounting for 91.76% of the genetic variation. In addition, population expansion tests (mismatch distribution and Fu’s Fs statistic) supported these results suggesting at least one population expansion.

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Genetic Diversity and Phylogenetic Relationships of Annual and Perennial Glycine Species

10.1101/557439 ◽

2019 ◽

Author(s):

Eun-Young Hwang ◽

He Wei ◽

Steven G. Schroeder ◽

Edward W. Fickus ◽

Charles V. Quigley ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Nucleotide Diversity ◽

Population Expansion ◽

Orthologous Gene ◽

Evolutionary Selection ◽

Gene Sets ◽

Sister Clade ◽

The Face

ABSTRACTWe estimated average genetic diversity of two Glycine annual and six perennial species based upon 76 orthologous gene sets and performed phylogenetic analysis, divergence analysis and tests for departure from neutrality of the eight species using 52 orthologous gene sets. In addition, 367 orthologous gene sets were used to estimate the relationships of 11 G. canescens accessions. Among the perennials, G. canescens showed the highest nucleotide diversity and the other perennials except G. tomentella had higher nucleotide diversity than the two annuals. Phylogenetic analysis of the Glycine showed a similar genome grouping with the previous report except G. cyrtoloba and G. stenophita formed a sister clade in the study. Divergence analysis supported the phylogenetic relationships, G. falcata was the most divergent from G. max, followed by G. cyrtoloba, G. syndetika, G. tomentella D3, G. stenophita and G. canescens. Neutrality selection tests within species showed that most genes were subjected to a recent directional selection due to a selective sweep or rapid population expansion. Although most gene sequence had negative and significant Tajima’s D, the sequences were homogeneous in the levels of polymorphism and divergence between G. max and other Glycine species based on the HKA test, thus, Glycine perennials may have experienced very similar evolutionary selection as inferred by trans-specific mutation analysis. The greater genetic diversity of most perennial Glycine species and their origins from the warmer and drier climates of Australia suggested the perennials as potential sources of heat and drought resistance that will be of value in the face of climate change.

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Diversitas Genetika dan Identifikasi Jenis Kelamin Burung Pelikan (Pelecanus conspicillatus Temminck, 1824) di Penangkaran Taman Margasatwa Ragunan Jakarta

Jurnal Biologi Indonesia ◽

10.47349/jbi/17022021/105 ◽

2021 ◽

Vol 17 (2) ◽

pp. 105-114

Author(s):

Anik Budhi Dharmayanthi ◽

Achmad Muchsinin ◽

Afriana Pulungan ◽

Moch Syamsul Arifin Zein

Keyword(s):

Genetic Diversity ◽

Nucleotide Diversity ◽

Haplotype Diversity ◽

Population Expansion ◽

Bird Populations ◽

Low Genetic Diversity ◽

In Captivity ◽

D Loop ◽

Haplotype 1

Pelicans (Pelecanus conspicillatus) is one of the wild species that have a widely distribution. This bird has been successfully bred in Ragunan Zoo, Jakarta. The indicator of inbreeding in the captive population is shown by the decrease of nucleotide diversity and number of haplotypes. The result of genetic diversity analysis using D-loop fragment sequences showed low genetic diversity with nucleotide diversity (p) = 0.00064 ± 0.00010 and haplotype diversity (Hd) = 0.532 ± 0.061 in Pelecanus conspicillatus populations in the Ragunan Zoo. However, negative Fu's Fs value (-3,246) indicates population expansion. We found that there were seven haplotypes in bird populations in the captivity: haplotype 1, 2 and 3 consist of 43 individuals (65.15%), five individuals (7.57%), and 14 individuals (21.21%), respectively. For each haplotype 4, 5, 6 and 7 is only represented by one individual of Pelecanus conspicillatus (1.51%). The sex ratio of males to females is 1: 8.86 with four males identified as haplotype 1, and one male on haplotypes 3, 5 and 7, respectively. Genetic diversity data of the population is an important way for designing long-term plans and goals in efforts to maintain genetic diversity of the Pelecanus conspicillatus population in captivity.

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Two species of Southeast Asian cats in the genus Catopuma with diverging histories: an island endemic forest specialist and a widespread habitat generalist

Royal Society Open Science ◽

10.1098/rsos.160350 ◽

2016 ◽

Vol 3 (10) ◽

pp. 160350 ◽

Cited By ~ 4

Author(s):

Riddhi P. Patel ◽

Daniel W. Förster ◽

Andrew C. Kitchener ◽

Mark D. Rayan ◽

Shariff W. Mohamed ◽

...

Keyword(s):

Late Pleistocene ◽

Species Distribution ◽

Nucleotide Diversity ◽

Demographic History ◽

Population Expansion ◽

Molecular Data ◽

Peninsular Malaysia ◽

Sister Species ◽

Morphological Data ◽

Island Endemic

Background. The bay cat Catopuma badia is endemic to Borneo, whereas its sister species the Asian golden cat Catopuma temminckii is distributed from the Himalayas and southern China through Indochina, Peninsular Malaysia and Sumatra. Based on morphological data, up to five subspecies of the Asian golden cat have been recognized, but a taxonomic assessment, including molecular data and morphological characters, is still lacking. Results. We combined molecular data (whole mitochondrial genomes), morphological data (pelage) and species distribution projections (up to the Late Pleistocene) to infer how environmental changes may have influenced the distribution of these sister species over the past 120 000 years. The molecular analysis was based on sequenced mitogenomes of 3 bay cats and 40 Asian golden cats derived mainly from archival samples. Our molecular data suggested a time of split between the two species approximately 3.16 Ma and revealed very low nucleotide diversity within the Asian golden cat population, which supports recent expansion of the population. Discussion. The low nucleotide diversity suggested a population bottleneck in the Asian golden cat, possibly caused by the eruption of the Toba volcano in Northern Sumatra (approx. 74 kya), followed by a continuous population expansion in the Late Pleistocene/Early Holocene. Species distribution projections, the reconstruction of the demographic history, a genetic isolation-by-distance pattern and a gradual variation of pelage pattern support the hypothesis of a post-Toba population expansion of the Asian golden cat from south China/Indochina to Peninsular Malaysia and Sumatra. Our findings reject the current classification of five subspecies for the Asian golden cat, but instead support either a monotypic species or one comprising two subspecies: (i) the Sunda golden cat, distributed south of the Isthmus of Kra: C. t. temminckii and (ii) Indochinese, Indian, Himalayan and Chinese golden cats, occurring north of the Isthmus: C. t. moormensis .

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Patterns of Nucleotide Diversity of theldpACircadian Gene in Closely Related Species of Cyanobacteria from Extreme Cold Deserts

Applied and Environmental Microbiology ◽

10.1128/aem.03439-12 ◽

2012 ◽

Vol 79 (5) ◽

pp. 1516-1522 ◽

Cited By ~ 3

Author(s):

Ka Wai Ng ◽

Stephen B. Pointing ◽

Volodymyr Dvornyk

Keyword(s):

Related Species ◽

Nucleotide Diversity ◽

Population Expansion ◽

Nucleotide Polymorphism ◽

Effective Population ◽

Closely Related Species ◽

Content Type ◽

Population Sizes ◽

Extreme Cold ◽

Small Effective Population Size

ABSTRACTIn the circadian system of cyanobacteria, theldpAgene is a component of the input to the clock. We comparatively analyzed nucleotide polymorphism of this gene in populations of two closely related species of cyanobacteria (denoted asSynechococcusspecies S1 and S2, respectively) from extreme cold deserts in Antarctica, the Canadian Arctic, and Tibet. Although both species manifested similarly high haplotype diversities (0.990 and 0.809, respectively), the nucleotide diversity differed significantly (0.0091 in S1 and 0.0037 in S2). The populations of species S2 were more differentiated (FST= 0.2242) compared to those of species S1 (FSTbetween 0.0296 and 0.1188). An analysis of positive selection with several tests yielded highly significant values (P< 0.01) for both species. On the other hand, these results may be somewhat compromised by fluctuating population sizes of the species. The apparent selection pressure coupled with the pronounced demographic factors, such as population expansion, small effective population size, and genetic drift, may thus result in the observed significant interpopulation differentiation and subsequent speciation of cyanobacteria.

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Evidence of male-biased dispersal in eastern grey kangaroos (Macropus giganteus)

Australian Journal of Zoology ◽

10.1071/zo16047 ◽

2016 ◽

Vol 64 (5) ◽

pp. 360 ◽

Cited By ~ 1

Author(s):

Brett A. Coghlan ◽

Jennifer M. Seddon ◽

Emily C. Best ◽

Vicki A. Thomson ◽

Anne W. Goldizen

Keyword(s):

National Park ◽

Nucleotide Diversity ◽

Genetic Relatedness ◽

Local Population ◽

Microsatellite Data ◽

Genetic Studies ◽

Female Philopatry ◽

Control Region Sequences ◽

Microsatellite Alleles ◽

Mtdna Haplotype

Dispersal reduces the likelihood of inbreeding and maintains gene flow among populations. Many polygynous mammals exhibit male-biased dispersal with female philopatry. Previous observational studies of eastern grey kangaroos (Macropus giganteus) suggested female philopatry while genetic studies showed weak structuring. We tested for sex-biased dispersal using two Queensland populations of kangaroos: one in Sundown National Park and the second at Elanda Point, Australia. Samples from 25 females and 23 males were collected from Sundown National Park, and analysed for partial mtDNA control region sequences (n = 47) and genotypes based on 12 microsatellite loci (n = 41). Samples from 18 males and 22 females from Elanda Point were genotyped at 8 loci and a subset sequenced for mtDNA (n = 19). Analyses showed higher mtDNA haplotype and nucleotide diversity in males than females within both populations, genetic relatedness based on microsatellite data was significantly higher among females, and microsatellite allelic richness was higher in males, suggesting that females are more likely to be philopatric and males more likely to disperse. These findings reinforce the value of including multiple types of genetic markers in dispersal analyses as mtDNA results showed higher male diversity (suggesting male dispersal) but males also contributed microsatellite alleles to the local population, masking differentiation between the sexes and confounding analyses.

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Molecular Diversity and Evolutionary Processes of Alternaria solani in Brazil Inferred Using Genealogical and Coalescent Approaches

Phytopathology ◽

10.1094/phyto-99-6-0765 ◽

2009 ◽

Vol 99 (6) ◽

pp. 765-774 ◽

Cited By ~ 23

Author(s):

Valdir Lourenço ◽

Andrés Moya ◽

Fernando González-Candelas ◽

Ignazio Carbone ◽

Luiz A. Maffia ◽

...

Keyword(s):

Gene Flow ◽

Nucleotide Diversity ◽

Early Blight ◽

Balancing Selection ◽

Haplotype Diversity ◽

Population Expansion ◽

Alternaria Solani ◽

Interesting Case ◽

Evolutionary Processes ◽

Tomato Plants

Alternaria spp. form a heterogeneous group of saprophytic and plant-pathogenic fungi widespread in temperate and tropical regions. However, the relationship between evolutionary processes and genetic diversity with epidemics is unknown for several plant-pathogenic Alternaria spp. The interaction of Alternaria solani populations with potato and tomato plants is an interesting case study for addressing questions related to molecular evolution of an asexual fungus. Gene genealogies based on the coalescent process were used to infer evolutionary processes that shape the A. solani population. Sequences of the rDNA internal transcribed spacer (ITS) region and the genes which encode the allergenic protein alt a 1 (Alt a 1) and glyceraldehyde-3-phosphate dehydrogenase (Gpd) were used to estimate haplotype and nucleotide diversity as well as for the coalescent analyses. The highest number of parsimony informative sites (n = 14), nucleotide diversity (0.007), and the average number of nucleotide differences (3.20) were obtained for Alt a 1. Although the highest number of haplotypes (n = 7) was generated for ITS, haplotype diversity was the lowest (0.148) for this region. Recombination was not detected. Subdivision was inferred from populations associated with hosts but there was no evidence of geographic subdivision, and gene flow is occurring among subpopulations. In the analysis of the Alt a 1, balancing selection and population expansion or purifying selection could have occurred in A. solani subpopulations associated with potato and tomato plants, respectively. There is strong evidence that the subpopulation of A. solani that causes early blight in potato is genetically distinct from the subpopulation that causes early blight in tomato. The population of A. solani is clonal, and gene flow and mutation are the main evolutionary processes shaping its genetic structure.

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MtDNA variation within local human populations in Bosnia and Herzegovina

Genetika ◽

10.2298/gensr1401209k ◽

2014 ◽

Vol 46 (1) ◽

pp. 209-218

Author(s):

Lejla Kapur-Pojskic ◽

Naris Pojskic ◽

Gabrijela Radosavljevic ◽

Damir Marjanovic ◽

Rifat Hadziselimovic

Keyword(s):

Bosnia And Herzegovina ◽

Nucleotide Diversity ◽

Human Populations ◽

Informative Marker ◽

Mountain Area ◽

Mtdna Variation ◽

Buccal Swabs ◽

Nj Tree ◽

Population Demographic ◽

Mtdna Haplotype

Being a crossroad of many ancient and recent historical migrations, Bosnia and Herzegovina (B&H) represents unique spot of multicultural and social diversity. The main aim of this study was to assess genetic structure of three local populations of mountain area from central part of B&H using mtDNA HVS-1 as an informative marker for population genetics studies. A 444 bp HVS-1 segment of control region of mtDNA extracted from buccal swabs was PCR amplified and sequenced. Haplotype and nucleotide diversity, average number of nucleotide differences, AMOVA and pairwise FST based on mtDNA haplotype and haplogroup frequencies were calculated. NJ tree was constructed based on pairwise FST results. Tajima?s D was calculated to evaluate population demographic status.

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Dynamics of the mtDNA Haplotype Variability in a Drosophila subobscura Population Over a Two-Year Period~!2010-03-29~!2010-05-10~!2010-06-24~!

The Open Evolution Journal ◽

10.2174/1874404401004010023 ◽

2010 ◽

Vol 4 (1) ◽

pp. 23-30 ◽

Cited By ~ 4

Author(s):

John S. Christie ◽

Antonia Picornell ◽

Andres Moya ◽

Maria M. Ramon ◽

Jose A. Castro

Keyword(s):

Drosophila Subobscura ◽

Mtdna Haplotype

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